TED toolkit: a comprehensive approach for convenient transcriptomic profiling as a clinically-oriented application
- Published
- Accepted
- Subject Areas
- Bioinformatics, Genomics, Translational Medicine, Computational Science, Data Science
- Keywords
- Transcriptome, Bioinformatics, Galaxy, RNA-sequencing, Workflow, Data Analysis
- Copyright
- © 2017 Ali et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. TED toolkit: a comprehensive approach for convenient transcriptomic profiling as a clinically-oriented application. PeerJ Preprints 5:e3385v1 https://doi.org/10.7287/peerj.preprints.3385v1
Abstract
In translational medicine, the technology of RNA sequencing (RNA-seq) continues to prove powerful, and transforming the RNA-seq data into biological insights has become increasingly imperative. We present the Transcriptomics profiler for Easy Discovery (TED) toolkit, a comprehensive approach to processing and analyzing RNA-seq data. TED is divided into three major modules: data quality control, transcriptome data analysis, and data discovery, with eleven pipelines in total. These pipelines perform the preliminary steps from assessing and correcting the quality of the RNA-seq data, to the simultaneous analysis of five transcriptomic features (differentially expressed coding, non-coding, novel isoform genes, gene fusions, alternative splicing events, genetic variants of somatic and germline mutations) and ultimately translating the RNA-seq analysis findings into actionable, clinically-relevant reports. TED was evaluated using previously published prostate cancer transcriptome data where we observed previously studied outcomes, and also created a knowledge database of highly-integrated, biologically relevant reports demonstrating that it is well-positioned for clinical applications. TED is implemented on an instance of the Galaxy platform (Galaxy page: http://galaxy.hunter.cuny.edu/u/bioitcore/p/transcriptomics-profiler-for-easy-discovery-ted-toolkit , Documentation Manual: http://ted.readthedocs.io/en/latest/index.html ) as intuitive and reproducible pipelines providing a manageable strategy for conducting substantial transcriptome analysis in a routine and sustainable fashion for bioinformatics researchers and clinicians alike.
Author Comment
This is a preprint submission to PeerJ Preprints.